Correlation between mRNAseq expression and clinical features
Thyroid Adenocarcinoma (Primary solid tumor)
23 September 2013  |  analyses__2013_09_23
Maintainer Information
Citation Information
doi:10.7908/C18G8J3C
Maintained by Juok Cho (Broad Institute)
Cite as Broad Institute TCGA Genome Data Analysis Center (2013): Correlation between mRNAseq expression and clinical features. Broad Institute of MIT and Harvard. doi:10.7908/C18G8J3C
Overview
Introduction

This pipeline uses various statistical tests to identify mRNAs whose expression levels correlated to selected clinical features.

Summary

Testing the association between 17997 genes and 15 clinical features across 463 samples, statistically thresholded by Q value < 0.05, 13 clinical features related to at least one genes.

  • 101 genes correlated to 'AGE'.

    • ZNF518B|85460 ,  RANBP17|64901 ,  MSL3L2|151507 ,  C12ORF52|84934 ,  IL20RA|53832 ,  ...

  • 450 genes correlated to 'NEOPLASM.DISEASESTAGE'.

    • GSPT2|23708 ,  FAM50B|26240 ,  SEMA3G|56920 ,  ZNF518B|85460 ,  GJA5|2702 ,  ...

  • 482 genes correlated to 'PATHOLOGY.T.STAGE'.

    • FBXO9|26268 ,  VIPR1|7433 ,  ZFP3|124961 ,  SLCO2A1|6578 ,  LTF|4057 ,  ...

  • 2263 genes correlated to 'PATHOLOGY.N.STAGE'.

    • CREB5|9586 ,  CLCNKA|1187 ,  SFTPB|6439 ,  FN1|2335 ,  MLEC|9761 ,  ...

  • 14 genes correlated to 'PATHOLOGY.M.STAGE'.

    • C4ORF6|10141 ,  CYP21A2|1589 ,  SLC27A6|28965 ,  KYNU|8942 ,  ST6GALNAC1|55808 ,  ...

  • 41 genes correlated to 'GENDER'.

    • RPS4Y1|6192 ,  ZFY|7544 ,  DDX3Y|8653 ,  NLGN4Y|22829 ,  UTY|7404 ,  ...

  • 5613 genes correlated to 'HISTOLOGICAL.TYPE'.

    • TM7SF4|81501 ,  ITGA3|3675 ,  FN1|2335 ,  ERBB3|2065 ,  SFTPB|6439 ,  ...

  • 28 genes correlated to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

    • C14ORF180|400258 ,  FLJ37543|285668 ,  ADIPOQ|9370 ,  TAS2R43|259289 ,  HPR|3250 ,  ...

  • 6 genes correlated to 'RADIATIONEXPOSURE'.

    • CRNN|49860 ,  RNF17|56163 ,  CSNK1A1P|161635 ,  CYORF15A|246126 ,  EIF1AY|9086 ,  ...

  • 1036 genes correlated to 'EXTRATHYROIDAL.EXTENSION'.

    • ZNF518B|85460 ,  ASAH2|56624 ,  SLC25A42|284439 ,  SRPX2|27286 ,  COL1A1|1277 ,  ...

  • 2 genes correlated to 'COMPLETENESS.OF.RESECTION'.

    • CATSPER2P1|440278 ,  SHOX2|6474

  • 1305 genes correlated to 'NUMBER.OF.LYMPH.NODES'.

    • CBFB|865 ,  FAM60A|58516 ,  PELI1|57162 ,  TAGLN2|8407 ,  CREB5|9586 ,  ...

  • 9 genes correlated to 'TUMOR.SIZE'.

    • ZC3H10|84872 ,  C3ORF32|51066 ,  ISLR2|57611 ,  FOXI2|399823 ,  CLDN2|9075 ,  ...

  • No genes correlated to 'Time to Death', and 'MULTIFOCALITY'.

Results
Overview of the results

Complete statistical result table is provided in Supplement Table 1

Table 1.  Get Full Table This table shows the clinical features, statistical methods used, and the number of genes that are significantly associated with each clinical feature at Q value < 0.05.

Clinical feature Statistical test Significant genes Associated with                 Associated with
Time to Death Cox regression test   N=0        
AGE Spearman correlation test N=101 older N=38 younger N=63
NEOPLASM DISEASESTAGE ANOVA test N=450        
PATHOLOGY T STAGE Spearman correlation test N=482 higher stage N=80 lower stage N=402
PATHOLOGY N STAGE t test N=2263 class1 N=1106 class0 N=1157
PATHOLOGY M STAGE ANOVA test N=14        
GENDER t test N=41 male N=19 female N=22
HISTOLOGICAL TYPE ANOVA test N=5613        
RADIATIONS RADIATION REGIMENINDICATION t test N=28 yes N=17 no N=11
RADIATIONEXPOSURE t test N=6 yes N=3 no N=3
EXTRATHYROIDAL EXTENSION ANOVA test N=1036        
COMPLETENESS OF RESECTION ANOVA test N=2        
NUMBER OF LYMPH NODES Spearman correlation test N=1305 higher number.of.lymph.nodes N=728 lower number.of.lymph.nodes N=577
MULTIFOCALITY t test   N=0        
TUMOR SIZE Spearman correlation test N=9 higher tumor.size N=0 lower tumor.size N=9
Clinical variable #1: 'Time to Death'

No gene related to 'Time to Death'.

Table S1.  Basic characteristics of clinical feature: 'Time to Death'

Time to Death Duration (Months) 0-158.8 (median=14.1)
  censored N = 445
  death N = 13
     
  Significant markers N = 0
Clinical variable #2: 'AGE'

101 genes related to 'AGE'.

Table S2.  Basic characteristics of clinical feature: 'AGE'

AGE Mean (SD) 47.03 (16)
  Significant markers N = 101
  pos. correlated 38
  neg. correlated 63
List of top 10 genes significantly correlated to 'AGE' by Spearman correlation test

Table S3.  Get Full Table List of top 10 genes significantly correlated to 'AGE' by Spearman correlation test

SpearmanCorr corrP Q
ZNF518B|85460 -0.341 4.501e-14 8.1e-10
RANBP17|64901 -0.3245 9.723e-13 1.75e-08
MSL3L2|151507 -0.3199 1.778e-12 3.2e-08
C12ORF52|84934 0.3026 2.921e-11 5.26e-07
IL20RA|53832 0.294 1.216e-10 2.19e-06
HCG11|493812 -0.2924 1.407e-10 2.53e-06
STL|7955 -0.2853 4.049e-10 7.29e-06
ASB13|79754 0.2815 7.034e-10 1.27e-05
LHFPL4|375323 0.2901 1.143e-09 2.06e-05
DDIT4L|115265 0.2775 1.286e-09 2.31e-05

Figure S1.  Get High-res Image As an example, this figure shows the association of ZNF518B|85460 to 'AGE'. P value = 4.5e-14 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #3: 'NEOPLASM.DISEASESTAGE'

450 genes related to 'NEOPLASM.DISEASESTAGE'.

Table S4.  Basic characteristics of clinical feature: 'NEOPLASM.DISEASESTAGE'

NEOPLASM.DISEASESTAGE Labels N
  STAGE I 263
  STAGE II 50
  STAGE III 102
  STAGE IV 2
  STAGE IVA 39
  STAGE IVC 5
     
  Significant markers N = 450
List of top 10 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'

Table S5.  Get Full Table List of top 10 genes differentially expressed by 'NEOPLASM.DISEASESTAGE'

ANOVA_P Q
GSPT2|23708 1.194e-14 2.15e-10
FAM50B|26240 1.691e-13 3.04e-09
SEMA3G|56920 3.62e-13 6.51e-09
ZNF518B|85460 1.766e-12 3.18e-08
GJA5|2702 2.437e-11 4.39e-07
SLC10A4|201780 2.745e-11 4.94e-07
PIK3R3|8503 2.795e-11 5.03e-07
CYP26A1|1592 5.036e-11 9.06e-07
ANXA3|306 1.454e-10 2.62e-06
MOGS|7841 1.741e-10 3.13e-06

Figure S2.  Get High-res Image As an example, this figure shows the association of GSPT2|23708 to 'NEOPLASM.DISEASESTAGE'. P value = 1.19e-14 with ANOVA analysis.

Clinical variable #4: 'PATHOLOGY.T.STAGE'

482 genes related to 'PATHOLOGY.T.STAGE'.

Table S6.  Basic characteristics of clinical feature: 'PATHOLOGY.T.STAGE'

PATHOLOGY.T.STAGE Mean (SD) 2.13 (0.88)
  N
  1 134
  2 154
  3 154
  4 19
     
  Significant markers N = 482
  pos. correlated 80
  neg. correlated 402
List of top 10 genes significantly correlated to 'PATHOLOGY.T.STAGE' by Spearman correlation test

Table S7.  Get Full Table List of top 10 genes significantly correlated to 'PATHOLOGY.T.STAGE' by Spearman correlation test

SpearmanCorr corrP Q
FBXO9|26268 -0.3133 5.852e-12 1.05e-07
VIPR1|7433 -0.3036 2.754e-11 4.96e-07
ZFP3|124961 -0.2837 5.528e-10 9.95e-06
SLCO2A1|6578 -0.2836 5.606e-10 1.01e-05
LTF|4057 -0.2814 7.711e-10 1.39e-05
LOC653501|653501 -0.2799 9.607e-10 1.73e-05
SYT15|83849 -0.2772 1.407e-09 2.53e-05
FAM65C|140876 -0.277 1.438e-09 2.59e-05
CLCNKB|1188 -0.2762 1.627e-09 2.93e-05
ASTE1|28990 -0.2736 2.329e-09 4.19e-05

Figure S3.  Get High-res Image As an example, this figure shows the association of FBXO9|26268 to 'PATHOLOGY.T.STAGE'. P value = 5.85e-12 with Spearman correlation analysis.

Clinical variable #5: 'PATHOLOGY.N.STAGE'

2263 genes related to 'PATHOLOGY.N.STAGE'.

Table S8.  Basic characteristics of clinical feature: 'PATHOLOGY.N.STAGE'

PATHOLOGY.N.STAGE Labels N
  class0 210
  class1 207
     
  Significant markers N = 2263
  Higher in class1 1106
  Higher in class0 1157
List of top 10 genes differentially expressed by 'PATHOLOGY.N.STAGE'

Table S9.  Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGY.N.STAGE'

T(pos if higher in 'class1') ttestP Q AUC
CREB5|9586 9.2 2.525e-18 4.54e-14 0.7287
CLCNKA|1187 -9 9.794e-18 1.76e-13 0.7295
SFTPB|6439 9.02 1.579e-17 2.84e-13 0.7104
FN1|2335 8.89 2.925e-17 5.26e-13 0.7147
MLEC|9761 -8.87 3.505e-17 6.31e-13 0.7228
KCNN4|3783 8.86 3.855e-17 6.94e-13 0.7178
CBFB|865 8.83 4.795e-17 8.63e-13 0.7506
TMEM117|84216 8.7 8.262e-17 1.49e-12 0.7244
TMPRSS4|56649 8.6 2.821e-16 5.07e-12 0.715
PELI1|57162 8.49 3.866e-16 6.96e-12 0.7251

Figure S4.  Get High-res Image As an example, this figure shows the association of CREB5|9586 to 'PATHOLOGY.N.STAGE'. P value = 2.52e-18 with T-test analysis.

Clinical variable #6: 'PATHOLOGY.M.STAGE'

14 genes related to 'PATHOLOGY.M.STAGE'.

Table S10.  Basic characteristics of clinical feature: 'PATHOLOGY.M.STAGE'

PATHOLOGY.M.STAGE Labels N
  M0 250
  M1 8
  MX 204
     
  Significant markers N = 14
List of top 10 genes differentially expressed by 'PATHOLOGY.M.STAGE'

Table S11.  Get Full Table List of top 10 genes differentially expressed by 'PATHOLOGY.M.STAGE'

ANOVA_P Q
C4ORF6|10141 4.967e-08 0.000894
CYP21A2|1589 6.469e-07 0.0116
SLC27A6|28965 6.487e-07 0.0117
KYNU|8942 8.236e-07 0.0148
ST6GALNAC1|55808 8.345e-07 0.015
SELP|6403 9.237e-07 0.0166
FAM111A|63901 1.44e-06 0.0259
ERP27|121506 1.491e-06 0.0268
SERPING1|710 1.732e-06 0.0312
RARRES1|5918 1.831e-06 0.0329

Figure S5.  Get High-res Image As an example, this figure shows the association of C4ORF6|10141 to 'PATHOLOGY.M.STAGE'. P value = 4.97e-08 with ANOVA analysis.

Clinical variable #7: 'GENDER'

41 genes related to 'GENDER'.

Table S12.  Basic characteristics of clinical feature: 'GENDER'

GENDER Labels N
  FEMALE 340
  MALE 123
     
  Significant markers N = 41
  Higher in MALE 19
  Higher in FEMALE 22
List of top 10 genes differentially expressed by 'GENDER'

Table S13.  Get Full Table List of top 10 genes differentially expressed by 'GENDER'

T(pos if higher in 'MALE') ttestP Q AUC
RPS4Y1|6192 88.8 4.641e-196 8.35e-192 1
ZFY|7544 91 6.318e-192 1.14e-187 1
DDX3Y|8653 95.74 1.725e-177 3.1e-173 1
NLGN4Y|22829 64.59 7.911e-150 1.42e-145 1
UTY|7404 89.77 1.338e-145 2.41e-141 1
PRKY|5616 40.96 9.405e-134 1.69e-129 0.9935
KDM5D|8284 82.49 6.966e-130 1.25e-125 1
USP9Y|8287 70.53 9.339e-118 1.68e-113 0.9999
XIST|7503 -46.87 1.494e-84 2.69e-80 0.9938
KDM5C|8242 -22.02 4.703e-59 8.46e-55 0.9402

Figure S6.  Get High-res Image As an example, this figure shows the association of RPS4Y1|6192 to 'GENDER'. P value = 4.64e-196 with T-test analysis.

Clinical variable #8: 'HISTOLOGICAL.TYPE'

5613 genes related to 'HISTOLOGICAL.TYPE'.

Table S14.  Basic characteristics of clinical feature: 'HISTOLOGICAL.TYPE'

HISTOLOGICAL.TYPE Labels N
  OTHER SPECIFY 9
  THYROID PAPILLARY CARCINOMA - CLASSICAL/USUAL 321
  THYROID PAPILLARY CARCINOMA - FOLLICULAR (>= 99% FOLLICULAR PATTERNED) 99
  THYROID PAPILLARY CARCINOMA - TALL CELL (>= 50% TALL CELL FEATURES) 34
     
  Significant markers N = 5613
List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

Table S15.  Get Full Table List of top 10 genes differentially expressed by 'HISTOLOGICAL.TYPE'

ANOVA_P Q
TM7SF4|81501 3.161e-46 5.69e-42
ITGA3|3675 3.534e-46 6.36e-42
FN1|2335 6.794e-45 1.22e-40
ERBB3|2065 1.309e-43 2.36e-39
SFTPB|6439 6.117e-43 1.1e-38
TMPRSS4|56649 1.175e-42 2.11e-38
FAM176A|84141 8.244e-42 1.48e-37
SERPINA1|5265 9.173e-42 1.65e-37
KCNN4|3783 1.154e-41 2.08e-37
UNC5CL|222643 1.473e-41 2.65e-37

Figure S7.  Get High-res Image As an example, this figure shows the association of TM7SF4|81501 to 'HISTOLOGICAL.TYPE'. P value = 3.16e-46 with ANOVA analysis.

Clinical variable #9: 'RADIATIONS.RADIATION.REGIMENINDICATION'

28 genes related to 'RADIATIONS.RADIATION.REGIMENINDICATION'.

Table S16.  Basic characteristics of clinical feature: 'RADIATIONS.RADIATION.REGIMENINDICATION'

RADIATIONS.RADIATION.REGIMENINDICATION Labels N
  NO 13
  YES 450
     
  Significant markers N = 28
  Higher in YES 17
  Higher in NO 11
List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

Table S17.  Get Full Table List of top 10 genes differentially expressed by 'RADIATIONS.RADIATION.REGIMENINDICATION'

T(pos if higher in 'YES') ttestP Q AUC
C14ORF180|400258 13.65 1.206e-13 2.16e-09 0.891
FLJ37543|285668 14.64 3.176e-13 5.7e-09 0.8861
ADIPOQ|9370 11.22 1.768e-11 3.17e-07 0.9185
TAS2R43|259289 9.75 6.674e-11 1.2e-06 0.7835
HPR|3250 11.38 4.804e-09 8.62e-05 0.9287
ENPP3|5169 9.48 1.749e-08 0.000314 0.8672
LOC440173|440173 9.29 2.379e-08 0.000427 0.8826
CXORF48|54967 9.01 1.968e-07 0.00353 0.8368
C6ORF203|51250 8.73 2.675e-07 0.0048 0.8737
HCFC1|3054 -8.85 3.192e-07 0.00573 0.8995

Figure S8.  Get High-res Image As an example, this figure shows the association of C14ORF180|400258 to 'RADIATIONS.RADIATION.REGIMENINDICATION'. P value = 1.21e-13 with T-test analysis.

Clinical variable #10: 'RADIATIONEXPOSURE'

6 genes related to 'RADIATIONEXPOSURE'.

Table S18.  Basic characteristics of clinical feature: 'RADIATIONEXPOSURE'

RADIATIONEXPOSURE Labels N
  NO 390
  YES 17
     
  Significant markers N = 6
  Higher in YES 3
  Higher in NO 3
List of 6 genes differentially expressed by 'RADIATIONEXPOSURE'

Table S19.  Get Full Table List of 6 genes differentially expressed by 'RADIATIONEXPOSURE'

T(pos if higher in 'YES') ttestP Q AUC
CRNN|49860 -11.3 2.904e-13 5.22e-09 0.9138
RNF17|56163 -8.31 6.257e-13 1.13e-08 0.875
CSNK1A1P|161635 -7.95 2.145e-12 3.86e-08 0.8147
CYORF15A|246126 6.8 2.898e-10 5.21e-06 0.6241
EIF1AY|9086 5.7 8.239e-08 0.00148 0.7721
TTTY15|64595 5.31 8.843e-07 0.0159 0.7211

Figure S9.  Get High-res Image As an example, this figure shows the association of CRNN|49860 to 'RADIATIONEXPOSURE'. P value = 2.9e-13 with T-test analysis.

Clinical variable #11: 'EXTRATHYROIDAL.EXTENSION'

1036 genes related to 'EXTRATHYROIDAL.EXTENSION'.

Table S20.  Basic characteristics of clinical feature: 'EXTRATHYROIDAL.EXTENSION'

EXTRATHYROIDAL.EXTENSION Labels N
  MINIMAL (T3) 120
  MODERATE/ADVANCED (T4A) 15
  NONE 314
  VERY ADVANCED (T4B) 1
     
  Significant markers N = 1036
List of top 10 genes differentially expressed by 'EXTRATHYROIDAL.EXTENSION'

Table S21.  Get Full Table List of top 10 genes differentially expressed by 'EXTRATHYROIDAL.EXTENSION'

ANOVA_P Q
ZNF518B|85460 1.326e-15 2.39e-11
ASAH2|56624 2.151e-15 3.87e-11
SLC25A42|284439 4.959e-15 8.92e-11
SRPX2|27286 1.917e-14 3.45e-10
COL1A1|1277 2.413e-14 4.34e-10
FAM69C|125704 3.85e-14 6.93e-10
COL3A1|1281 6.447e-14 1.16e-09
FLJ42875|440556 8.882e-14 1.6e-09
PRDM16|63976 1.157e-13 2.08e-09
FOXJ1|2302 1.51e-13 2.72e-09

Figure S10.  Get High-res Image As an example, this figure shows the association of ZNF518B|85460 to 'EXTRATHYROIDAL.EXTENSION'. P value = 1.33e-15 with ANOVA analysis.

Clinical variable #12: 'COMPLETENESS.OF.RESECTION'

2 genes related to 'COMPLETENESS.OF.RESECTION'.

Table S22.  Basic characteristics of clinical feature: 'COMPLETENESS.OF.RESECTION'

COMPLETENESS.OF.RESECTION Labels N
  R0 361
  R1 44
  R2 3
  RX 28
     
  Significant markers N = 2
List of 2 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'

Table S23.  Get Full Table List of 2 genes differentially expressed by 'COMPLETENESS.OF.RESECTION'

ANOVA_P Q
CATSPER2P1|440278 4.497e-08 0.000809
SHOX2|6474 1.338e-06 0.0241

Figure S11.  Get High-res Image As an example, this figure shows the association of CATSPER2P1|440278 to 'COMPLETENESS.OF.RESECTION'. P value = 4.5e-08 with ANOVA analysis.

Clinical variable #13: 'NUMBER.OF.LYMPH.NODES'

1305 genes related to 'NUMBER.OF.LYMPH.NODES'.

Table S24.  Basic characteristics of clinical feature: 'NUMBER.OF.LYMPH.NODES'

NUMBER.OF.LYMPH.NODES Mean (SD) 3.55 (6.2)
  Significant markers N = 1305
  pos. correlated 728
  neg. correlated 577
List of top 10 genes significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

Table S25.  Get Full Table List of top 10 genes significantly correlated to 'NUMBER.OF.LYMPH.NODES' by Spearman correlation test

SpearmanCorr corrP Q
CBFB|865 0.4041 8.318e-16 1.5e-11
FAM60A|58516 0.4017 1.272e-15 2.29e-11
PELI1|57162 0.4005 1.562e-15 2.81e-11
TAGLN2|8407 0.3855 2.045e-14 3.68e-10
CREB5|9586 0.385 2.229e-14 4.01e-10
S100A10|6281 0.3829 3.164e-14 5.69e-10
GPR153|387509 0.3771 8.201e-14 1.48e-09
FECH|2235 -0.3765 9.03e-14 1.62e-09
S100A4|6275 0.3712 2.111e-13 3.8e-09
ZNF346|23567 -0.3708 2.271e-13 4.09e-09

Figure S12.  Get High-res Image As an example, this figure shows the association of CBFB|865 to 'NUMBER.OF.LYMPH.NODES'. P value = 8.32e-16 with Spearman correlation analysis. The straight line presents the best linear regression.

Clinical variable #14: 'MULTIFOCALITY'

No gene related to 'MULTIFOCALITY'.

Table S26.  Basic characteristics of clinical feature: 'MULTIFOCALITY'

MULTIFOCALITY Labels N
  MULTIFOCAL 208
  UNIFOCAL 245
     
  Significant markers N = 0
Clinical variable #15: 'TUMOR.SIZE'

9 genes related to 'TUMOR.SIZE'.

Table S27.  Basic characteristics of clinical feature: 'TUMOR.SIZE'

TUMOR.SIZE Mean (SD) 2.94 (1.6)
  Significant markers N = 9
  pos. correlated 0
  neg. correlated 9
List of 9 genes significantly correlated to 'TUMOR.SIZE' by Spearman correlation test

Table S28.  Get Full Table List of 9 genes significantly correlated to 'TUMOR.SIZE' by Spearman correlation test

SpearmanCorr corrP Q
ZC3H10|84872 -0.2821 3.384e-08 0.000609
C3ORF32|51066 -0.2855 3.682e-08 0.000663
ISLR2|57611 -0.2798 4.434e-08 0.000798
FOXI2|399823 -0.2706 1.461e-07 0.00263
CLDN2|9075 -0.2662 2.344e-07 0.00422
LRRC55|219527 -0.2557 7.136e-07 0.0128
GGT5|2687 -0.2493 1.195e-06 0.0215
SLC14A1|6563 -0.2464 1.606e-06 0.0289
PI16|221476 -0.2445 2.345e-06 0.0422

Figure S13.  Get High-res Image As an example, this figure shows the association of ZC3H10|84872 to 'TUMOR.SIZE'. P value = 3.38e-08 with Spearman correlation analysis. The straight line presents the best linear regression.

Methods & Data
Input

  • Expresson data file = THCA-TP.uncv2.mRNAseq_RSEM_normalized_log2.txt

  • Clinical data file = THCA-TP.clin.merged.picked.txt

  • Number of patients = 463

  • Number of genes = 17997

  • Number of clinical features = 15

Survival analysis

For survival clinical features, Wald's test in univariate Cox regression analysis with proportional hazards model (Andersen and Gill 1982) was used to estimate the P values using the 'coxph' function in R. Kaplan-Meier survival curves were plot using the four quartile subgroups of patients based on expression levels

Correlation analysis

For continuous numerical clinical features, Spearman's rank correlation coefficients (Spearman 1904) and two-tailed P values were estimated using 'cor.test' function in R

ANOVA analysis

For multi-class clinical features (ordinal or nominal), one-way analysis of variance (Howell 2002) was applied to compare the log2-expression levels between different clinical classes using 'anova' function in R

Student's t-test analysis

For two-class clinical features, two-tailed Student's t test with unequal variance (Lehmann and Romano 2005) was applied to compare the log2-expression levels between the two clinical classes using 't.test' function in R

Q value calculation

For multiple hypothesis correction, Q value is the False Discovery Rate (FDR) analogue of the P value (Benjamini and Hochberg 1995), defined as the minimum FDR at which the test may be called significant. We used the 'Benjamini and Hochberg' method of 'p.adjust' function in R to convert P values into Q values.

Download Results

In addition to the links below, the full results of the analysis summarized in this report can also be downloaded programmatically using firehose_get, or interactively from either the Broad GDAC website or TCGA Data Coordination Center Portal.

References
[1] Andersen and Gill, Cox's regression model for counting processes, a large sample study, Annals of Statistics 10(4):1100-1120 (1982)
[2] Spearman, C, The proof and measurement of association between two things, Amer. J. Psychol 15:72-101 (1904)
[3] Howell, D, Statistical Methods for Psychology. (5th ed.), Duxbury Press:324-5 (2002)
[4] Lehmann and Romano, Testing Statistical Hypotheses (3E ed.), New York: Springer. ISBN 0387988645 (2005)
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